Workflow

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If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code
config.yaml 
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samples:
    path: "/tier4/DSC/GATK/DB/samples/"


ref:
    path: "/tier4/DSC/GATK/DB/references/hg19/"
    species: homo_sapiens
    release: 101
    build: GRCh37.p13
    version: "hg19" 

    
knowndb:
    dbSNP: "/tier4/DSC/GATK/DB/dbsnp_138.hg19.vcf"


readingtype: "paired" # either paired(default) or single 


filteroption: "hard" # either vqsr or hard


filtering:
    vqsr:  
        resources: # resources path 
            hapmap: "/tier4/DSC/GATK/DB/HapMap/hapmp_phase3_ensembl_v99_hg19_CHB_JPT.vcf" #CHB+JPT
            omni: "/tier4/DSC/GATK/DB/1000G_omni2.5.hg19.sites.vcf" 
            g1k: "/tier4/DSC/GATK/DB/1000G_phase1.snps.high_confidence.hg19.sites.vcf"
            dbsnp: "/tier4/DSC/GATK/DB/dbsnp_138.hg19.vcf"
            g1k_indel: ""
            
    hard:  
        snvs:
            "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"
        indels:
            "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"

   
processing:
    remove-duplicates: true
    # Uncomment and point to a bed file with, e.g., captured regions if necessary,
    # see https://gatkforums.broadinstitute.org/gatk/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals.
    # restrict-regions: captured_regions.bed
    # If regions are restricted, uncomment this to enlarge them by the given value in order to include
    # flanking areas.
    # region-padding: 100


params:
    bwa:
        readgroup: "-RGID inco -RGSM BRCA_NA12892 -RGLB BRCA_NA12892 -RGPU illumina  -RGPL illumina"
    gatk:
        HaplotypeCaller: "-ERC GVCF"
        GenomicsDBimport: "-merge-input-intervals true"
        BaseRecalibrator: ""
        GenotypeGVCFs: ""
        VariantRecalibrator:
                mode: "SNP"
                annotation: ["QD"] # which fields to use with -an
                extra: ""
        MarkDuplicates: "REMOVE_DUPLICATES false"
        Funcotator:
            path: ["/tier4/DSC/GATK/DB/Funcotator/funcotator_dataSources.v1.6.20190124g/"]
    trimmomatic:
        trimmer:
            - "LEADING:3"
            - "TRAILING:3"
            - "SLIDINGWINDOW:4:15"
            - "MINLEN:80"
        adapter: "/tier4/DSC/GATK/DB/adapters/TruSeq3-PE.fa" 
    vep:
        plugins:
            - LoFtool
        extra: ""

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